Contacts of the helix formed by residues 177 - 190 (chain A) in PDB entry 5I1U
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ALA 177 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A TYR* 3.5 40.6 - - + +
146A TYR* 3.6 21.1 - - + -
173A ARG 4.1 1.2 + - - -
174A GLY 3.3 11.8 + - - -
175A THR 3.2 3.2 - - - +
176A ALA* 1.3 78.9 - - - +
178A MET* 1.3 64.8 + - - +
179A GLU 3.2 2.9 - - - +
180A SER* 3.2 7.7 + - - +
181A ILE* 3.0 23.1 + - + +
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Residues in contact with MET 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A ARG 4.6 5.9 + - - +
176A ALA* 3.1 23.4 + - + +
177A ALA* 1.3 78.3 - - - +
179A GLU* 1.3 61.1 + - + +
181A ILE* 3.7 17.8 - - + +
182A PHE* 2.9 72.8 + - + +
210A ALA 4.2 7.0 - - - +
211A ALA* 3.6 35.7 - - + +
214A PRO* 4.7 7.0 - - + -
299A TRP* 3.7 34.1 - - + -
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Residues in contact with GLU 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ASN* 3.6 26.6 + - + +
145A TYR* 4.2 25.8 - - + -
173A ARG 5.4 2.8 + - - +
177A ALA* 3.2 1.4 - - - +
178A MET* 1.3 78.5 - - + +
180A SER* 1.3 57.8 + - - +
183A ASP* 2.9 27.4 + - - -
207A ARG* 2.8 49.1 + - - +
208A GLN* 4.3 15.8 + - - +
211A ALA* 4.5 13.7 - - - +
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Residues in contact with SER 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LEU* 6.1 0.2 - - - -
76A TYR* 3.3 22.4 - - - -
142A ASN* 3.7 27.9 + - - +
143A TRP* 3.7 24.4 + - - -
146A TYR* 5.3 2.3 - - - +
177A ALA* 3.2 8.1 + - - -
179A GLU* 1.3 75.0 - - - +
181A ILE* 1.3 59.8 + - - +
183A ASP* 3.1 14.0 + - - +
184A MET* 3.0 35.5 + - - +
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Residues in contact with ILE 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A TYR* 2.8 28.9 + - - +
72A LEU* 5.2 1.8 - - + -
73A MET* 4.3 21.1 - - + -
76A TYR* 3.7 29.2 - - + -
176A ALA 3.9 15.3 - - - +
177A ALA 3.0 20.0 + - - +
178A MET* 3.7 22.7 - - + +
180A SER* 1.3 74.0 - - - +
182A PHE* 1.3 62.3 + - + +
184A MET* 3.3 11.4 + - - +
185A ILE 3.8 1.7 + - - -
299A TRP* 3.2 44.2 - - + +
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Residues in contact with PHE 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A MET* 2.9 43.2 + - + +
179A GLU* 5.4 0.2 - - - -
181A ILE* 1.3 80.2 - - + +
183A ASP* 1.3 65.4 + - - +
184A MET 3.0 1.1 - - - -
185A ILE* 3.0 39.8 + - + +
186A GLU* 4.2 2.8 + - - +
207A ARG* 3.6 64.1 + - + +
210A ALA* 3.7 23.1 - - + -
211A ALA* 3.6 13.9 - - + -
292A TYR* 5.0 3.2 - - + -
296A MET* 4.3 12.1 - - + -
299A TRP* 3.8 29.8 - + + -
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Residues in contact with ASP 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A TRP* 3.4 29.1 - - + -
138A ARG* 2.8 37.0 + - - +
139A ALA* 3.5 21.5 - - + +
142A ASN* 2.9 25.0 + - - +
143A TRP* 6.0 0.2 - - - -
179A GLU 2.9 16.8 + - - +
180A SER* 3.3 12.0 - - - +
182A PHE* 1.3 74.6 - - - +
184A MET* 1.3 67.4 + - + +
185A ILE 3.2 0.9 + - - -
186A GLU* 3.2 14.4 + - - +
187A ARG 3.5 0.9 + - - -
207A ARG* 2.9 14.1 + - - +
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Residues in contact with MET 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A TYR* 3.5 16.2 - - + +
68A LEU* 5.7 2.2 - - - -
72A LEU* 3.7 28.9 - - + -
127A ILE* 3.4 47.8 - - + -
135A TRP* 3.6 19.3 - - + -
139A ALA* 5.7 0.4 - - + -
143A TRP* 5.6 3.8 - - - +
180A SER* 3.0 22.8 + - - +
181A ILE* 3.4 10.8 - - - +
182A PHE 3.0 0.8 - - - -
183A ASP* 1.3 76.4 - - + +
185A ILE* 1.3 59.1 + - - +
186A GLU 3.2 0.2 - - - -
187A ARG* 3.8 12.8 - - + +
188A LEU* 2.8 44.0 + - + +
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Residues in contact with ILE 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A TYR* 4.3 19.7 - - + -
181A ILE 3.8 0.4 + - - +
182A PHE* 3.0 33.7 + - + +
184A MET* 1.3 77.7 - - - +
186A GLU* 1.3 58.5 + - - +
188A LEU* 4.0 0.6 - - - -
189A GLY* 3.0 24.9 + - - -
191A PHE* 3.6 20.8 - - + -
291A ARG 4.3 12.8 - - - +
292A TYR* 4.4 13.7 - - + +
295A GLY* 3.7 12.8 - - - +
296A MET* 3.6 43.1 - - + +
299A TRP* 5.1 1.1 - - + -
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Residues in contact with GLU 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A MET* 3.9 3.1 - - + +
135A TRP* 3.0 25.0 + - - +
138A ARG* 2.8 30.7 + - - -
182A PHE 4.9 2.5 - - - +
183A ASP* 3.2 10.4 + - - +
185A ILE* 1.3 78.2 - - + +
187A ARG* 1.3 60.6 + - - +
189A GLY 3.3 0.2 + - - -
190A HIS* 2.8 26.2 + - - -
191A PHE* 3.1 34.6 + - + +
192A GLU* 3.4 5.5 - - - +
193A VAL* 2.9 51.6 + - + +
198A MET* 4.0 4.5 - - - +
207A ARG* 5.4 0.5 + - - -
292A TYR* 5.4 3.6 - - + -
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Residues in contact with ARG 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLU* 5.0 6.5 + - - -
65A ASP* 3.0 29.7 + - - -
68A LEU* 3.7 14.9 - - + +
126A ARG* 2.9 30.9 + - - +
127A ILE* 3.0 24.3 + - - +
129A LEU* 3.4 30.2 + - - +
131A MET* 3.7 16.4 - - - +
135A TRP* 4.1 7.4 - - + -
183A ASP 3.5 2.6 + - - -
184A MET* 3.3 27.9 + - + +
186A GLU* 1.3 78.4 - - - +
188A LEU* 1.3 70.9 + - + +
190A HIS* 3.3 26.3 + - - -
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Residues in contact with LEU 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A TYR* 3.7 48.2 - - + -
60A GLU 5.4 0.2 - - - +
61A SER* 4.2 24.5 - - - -
62A SER 5.1 0.3 + - - -
65A ASP* 3.5 46.2 - - + +
68A LEU* 4.1 23.1 - - + -
69A ALA* 4.0 13.0 - - + -
184A MET* 2.8 31.5 + - + +
185A ILE 4.6 0.9 - - - +
187A ARG* 1.3 79.3 - - + +
189A GLY* 1.3 57.8 + - - +
190A HIS* 3.5 4.2 - - - -
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Residues in contact with GLY 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A ILE 3.0 18.5 + - - -
187A ARG 3.2 0.2 - - - -
188A LEU* 1.3 78.0 - - - +
190A HIS* 1.3 72.0 + - - +
191A PHE* 3.4 8.0 + - - -
291A ARG* 2.8 33.2 + - - -
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Residues in contact with HIS 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ASP* 2.7 30.6 + - - -
129A LEU 5.9 1.6 - - - -
130A GLY* 6.4 0.2 - - - -
131A MET* 5.4 6.2 - - - -
186A GLU 2.8 8.9 + - - -
187A ARG* 3.3 23.7 + - - +
188A LEU 3.9 4.0 - - - -
189A GLY* 1.3 82.8 - - - +
191A PHE* 1.3 57.3 + - - +
291A ARG* 4.9 1.2 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il